FMO DATABASE

FMODB ID: RL488

Calculation Name: 2WP2-B-Xray547

Preferred Name:

Target Type:

Ligand Name: n(6)-acetyllysine

Ligand 3-letter code: ALY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2WP2

Chain ID: B

ChEMBL ID:

UniProt ID: Q91Y44

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	110
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-943784.681321
FMO2-HF: Nuclear repulsion	897272.223813
FMO2-HF: Total energy	-46512.457509
FMO2-MP2: Total energy	-46645.355532

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:27:LEU)

Summations of interaction energy for fragment #1(A:27:LEU)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
6.1789999999999	14.178	9.072	-4.197	-12.877	-0.032

Interaction energy analysis for fragmet #1(A:27:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.930

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	29	ASN	0	0.054	0.010	2.637	-4.504	-2.118	0.708	-1.272	-1.822	-0.012
4	A	30	GLN	0	0.020	0.010	5.282	-0.468	-0.316	-0.001	-0.006	-0.144	0.000
5	A	31	LEU	0	0.021	0.027	2.383	-0.113	0.838	3.627	-1.179	-3.399	-0.010
6	A	32	GLN	0	0.005	-0.007	2.484	7.345	7.862	3.123	-0.867	-2.774	-0.004
7	A	33	PHE	0	0.009	0.014	3.216	4.350	3.867	0.125	0.555	-0.197	0.000
9	A	35	GLN	0	0.010	0.009	4.242	1.718	1.994	-0.001	-0.016	-0.260	0.000
56	A	82	LEU	0	-0.019	-0.003	2.797	-5.571	-4.728	0.187	-0.207	-0.823	-0.002
57	A	83	GLU	-1	-0.862	-0.920	3.383	-28.416	-27.218	0.131	-0.598	-0.731	-0.005
59	A	85	LYS	1	0.859	0.923	2.477	52.047	53.576	1.176	-0.682	-2.025	0.001
60	A	86	TYR	0	0.006	0.019	3.460	-1.407	-1.475	-0.001	0.204	-0.135	0.000
61	A	87	TYR	0	-0.048	-0.059	4.373	1.198	1.378	-0.001	-0.022	-0.157	0.000
62	A	88	GLU	-1	-0.944	-0.963	4.135	-42.243	-41.834	0.000	-0.083	-0.326	0.000
63	A	89	LYS	1	0.855	0.897	4.445	20.378	20.487	-0.001	-0.024	-0.084	0.000
8	A	34	LEU	0	0.040	0.008	5.623	2.497	2.497	0.000	0.000	0.000	0.000
10	A	36	ARG	1	0.861	0.923	5.740	34.666	34.666	0.000	0.000	0.000	0.000
11	A	37	VAL	0	-0.035	-0.012	8.314	2.195	2.195	0.000	0.000	0.000	0.000
12	A	38	VAL	0	0.010	0.018	9.665	1.425	1.425	0.000	0.000	0.000	0.000
13	A	39	LEU	0	0.048	0.034	8.329	1.381	1.381	0.000	0.000	0.000	0.000
14	A	40	LYS	1	0.909	0.963	10.770	20.121	20.121	0.000	0.000	0.000	0.000
15	A	41	ALA	0	-0.027	-0.018	12.566	1.172	1.172	0.000	0.000	0.000	0.000
16	A	42	LEU	0	0.016	-0.001	14.264	0.847	0.847	0.000	0.000	0.000	0.000
17	A	43	TRP	0	-0.009	-0.003	13.410	0.323	0.323	0.000	0.000	0.000	0.000
18	A	44	LYS	1	0.911	0.954	16.286	15.202	15.202	0.000	0.000	0.000	0.000
19	A	45	HIS	0	0.035	0.045	18.718	0.528	0.528	0.000	0.000	0.000	0.000
20	A	46	GLY	0	0.030	0.012	20.799	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	47	PHE	0	-0.014	-0.023	23.455	0.318	0.318	0.000	0.000	0.000	0.000
22	A	48	SER	0	0.046	0.017	18.587	0.121	0.121	0.000	0.000	0.000	0.000
23	A	49	TRP	0	0.030	0.015	20.284	-0.335	-0.335	0.000	0.000	0.000	0.000
24	A	50	PRO	0	0.010	0.009	22.392	-0.071	-0.071	0.000	0.000	0.000	0.000
25	A	51	PHE	0	0.029	0.006	18.562	-0.047	-0.047	0.000	0.000	0.000	0.000
26	A	52	GLN	0	-0.057	-0.030	17.127	-0.847	-0.847	0.000	0.000	0.000	0.000
27	A	53	GLN	0	-0.069	-0.042	17.708	-0.427	-0.427	0.000	0.000	0.000	0.000
28	A	54	PRO	0	-0.010	0.001	18.001	0.195	0.195	0.000	0.000	0.000	0.000
29	A	55	VAL	0	0.026	0.024	20.198	0.388	0.388	0.000	0.000	0.000	0.000
30	A	56	ASP	-1	-0.798	-0.892	23.629	-10.055	-10.055	0.000	0.000	0.000	0.000
31	A	57	ALA	0	0.059	0.018	26.485	0.257	0.257	0.000	0.000	0.000	0.000
32	A	58	VAL	0	-0.006	0.011	29.434	0.347	0.347	0.000	0.000	0.000	0.000
33	A	59	LYS	1	0.829	0.899	27.244	10.387	10.387	0.000	0.000	0.000	0.000
34	A	60	LEU	0	-0.022	-0.016	27.304	0.239	0.239	0.000	0.000	0.000	0.000
35	A	61	LYS	1	0.888	0.957	31.787	8.134	8.134	0.000	0.000	0.000	0.000
36	A	62	LEU	0	0.029	0.027	29.109	0.130	0.130	0.000	0.000	0.000	0.000
37	A	63	PRO	0	-0.013	-0.013	31.630	-0.250	-0.250	0.000	0.000	0.000	0.000
38	A	64	ASP	-1	-0.803	-0.889	33.305	-8.843	-8.843	0.000	0.000	0.000	0.000
39	A	65	TYR	0	0.035	0.020	23.194	-0.222	-0.222	0.000	0.000	0.000	0.000
40	A	66	TYR	0	-0.027	-0.038	24.305	-0.112	-0.112	0.000	0.000	0.000	0.000
41	A	67	THR	0	-0.063	-0.017	27.996	-0.101	-0.101	0.000	0.000	0.000	0.000
42	A	68	ILE	0	-0.013	0.004	28.631	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	69	ILE	0	-0.076	-0.020	23.298	-0.326	-0.326	0.000	0.000	0.000	0.000
44	A	70	LYS	1	0.994	0.989	23.397	12.112	12.112	0.000	0.000	0.000	0.000
45	A	71	THR	0	-0.020	-0.018	19.053	-0.152	-0.152	0.000	0.000	0.000	0.000
46	A	72	PRO	0	0.004	0.013	19.996	-0.267	-0.267	0.000	0.000	0.000	0.000
47	A	73	MET	0	-0.024	0.005	13.911	-0.995	-0.995	0.000	0.000	0.000	0.000
48	A	74	ASP	-1	-0.766	-0.861	15.247	-15.365	-15.365	0.000	0.000	0.000	0.000
49	A	75	LEU	0	0.077	0.021	13.173	-1.236	-1.236	0.000	0.000	0.000	0.000
50	A	76	ASN	0	-0.042	-0.021	11.964	-1.940	-1.940	0.000	0.000	0.000	0.000
51	A	77	THR	0	-0.062	-0.055	11.913	-1.081	-1.081	0.000	0.000	0.000	0.000
52	A	78	ILE	0	0.025	0.009	8.741	-1.643	-1.643	0.000	0.000	0.000	0.000
53	A	79	LYS	1	0.807	0.886	7.590	17.666	17.666	0.000	0.000	0.000	0.000
54	A	80	LYS	1	0.955	0.978	7.189	15.124	15.124	0.000	0.000	0.000	0.000
55	A	81	ARG	1	0.858	0.930	7.187	19.923	19.923	0.000	0.000	0.000	0.000
58	A	84	ASN	0	-0.069	-0.045	5.763	-0.350	-0.350	0.000	0.000	0.000	0.000
64	A	90	ALA	0	0.020	-0.001	6.219	1.994	1.994	0.000	0.000	0.000	0.000
65	A	91	SER	0	0.071	0.031	7.393	1.416	1.416	0.000	0.000	0.000	0.000
66	A	92	GLU	-1	-0.789	-0.885	8.418	-30.592	-30.592	0.000	0.000	0.000	0.000
67	A	93	CYS	0	-0.034	-0.003	6.826	1.245	1.245	0.000	0.000	0.000	0.000
68	A	94	ILE	0	-0.009	-0.011	8.960	1.734	1.734	0.000	0.000	0.000	0.000
69	A	95	GLU	-1	-0.815	-0.903	12.002	-15.855	-15.855	0.000	0.000	0.000	0.000
70	A	96	ASP	-1	-0.766	-0.819	11.135	-20.540	-20.540	0.000	0.000	0.000	0.000
71	A	97	PHE	0	-0.023	-0.033	9.706	0.981	0.981	0.000	0.000	0.000	0.000
72	A	98	ASN	0	0.016	-0.001	14.321	1.428	1.428	0.000	0.000	0.000	0.000
73	A	99	THR	0	-0.034	-0.008	16.538	1.163	1.163	0.000	0.000	0.000	0.000
74	A	100	MET	0	-0.071	-0.022	16.290	0.616	0.616	0.000	0.000	0.000	0.000
75	A	101	PHE	0	0.012	-0.005	16.789	0.540	0.540	0.000	0.000	0.000	0.000
76	A	102	SER	0	0.018	-0.007	20.656	0.776	0.776	0.000	0.000	0.000	0.000
77	A	103	ASN	0	-0.036	-0.038	20.227	0.767	0.767	0.000	0.000	0.000	0.000
78	A	104	CYS	0	-0.085	-0.016	22.918	0.633	0.633	0.000	0.000	0.000	0.000
79	A	105	TYR	0	-0.039	-0.069	23.408	0.562	0.562	0.000	0.000	0.000	0.000
80	A	106	LEU	0	-0.014	0.015	26.316	0.329	0.329	0.000	0.000	0.000	0.000
81	A	107	TYR	0	-0.062	-0.053	27.607	0.257	0.257	0.000	0.000	0.000	0.000
82	A	108	ASN	0	-0.068	-0.038	27.202	0.483	0.483	0.000	0.000	0.000	0.000
83	A	109	LYS	1	0.966	0.981	30.448	7.826	7.826	0.000	0.000	0.000	0.000
84	A	110	THR	0	-0.001	-0.020	32.465	-0.191	-0.191	0.000	0.000	0.000	0.000
85	A	111	GLY	0	-0.014	-0.006	32.876	0.265	0.265	0.000	0.000	0.000	0.000
86	A	112	ASP	-1	-0.823	-0.892	31.659	-8.524	-8.524	0.000	0.000	0.000	0.000
87	A	113	ASP	-1	-0.883	-0.948	31.025	-8.909	-8.909	0.000	0.000	0.000	0.000
88	A	114	ILE	0	-0.009	-0.018	25.073	-0.312	-0.312	0.000	0.000	0.000	0.000
89	A	115	VAL	0	0.033	0.010	26.194	-0.496	-0.496	0.000	0.000	0.000	0.000
90	A	116	VAL	0	0.013	0.012	26.854	-0.312	-0.312	0.000	0.000	0.000	0.000
91	A	117	MET	0	-0.087	-0.040	24.954	-0.230	-0.230	0.000	0.000	0.000	0.000
92	A	118	ALA	0	0.014	0.007	22.353	-0.441	-0.441	0.000	0.000	0.000	0.000
93	A	119	GLN	0	0.056	0.031	22.279	-0.281	-0.281	0.000	0.000	0.000	0.000
94	A	120	ALA	0	-0.056	-0.023	23.689	-0.205	-0.205	0.000	0.000	0.000	0.000
95	A	121	LEU	0	-0.045	-0.019	18.784	-0.446	-0.446	0.000	0.000	0.000	0.000
96	A	122	GLU	-1	-0.806	-0.869	18.682	-13.572	-13.572	0.000	0.000	0.000	0.000
97	A	123	LYS	1	0.965	0.983	19.504	10.425	10.425	0.000	0.000	0.000	0.000
98	A	124	LEU	0	-0.040	-0.016	17.254	-0.237	-0.237	0.000	0.000	0.000	0.000
99	A	125	PHE	0	0.021	0.003	12.130	-0.762	-0.762	0.000	0.000	0.000	0.000
100	A	126	MET	0	0.021	0.005	15.586	-0.623	-0.623	0.000	0.000	0.000	0.000
101	A	127	GLN	0	-0.025	-0.010	17.776	-0.230	-0.230	0.000	0.000	0.000	0.000
102	A	128	LYS	1	0.919	0.966	13.565	15.036	15.036	0.000	0.000	0.000	0.000
103	A	129	LEU	0	0.023	0.006	11.770	-0.927	-0.927	0.000	0.000	0.000	0.000
104	A	130	SER	0	-0.062	-0.037	13.988	-0.301	-0.301	0.000	0.000	0.000	0.000
105	A	131	GLN	0	-0.049	-0.029	15.043	0.405	0.405	0.000	0.000	0.000	0.000
106	A	132	MET	0	-0.043	-0.004	9.430	-1.766	-1.766	0.000	0.000	0.000	0.000
107	A	133	PRO	0	-0.055	-0.023	9.027	0.673	0.673	0.000	0.000	0.000	0.000
108	A	134	GLN	0	0.004	-0.013	11.150	-0.833	-0.833	0.000	0.000	0.000	0.000
109	A	135	GLU	-1	-0.956	-0.992	11.591	-22.700	-22.700	0.000	0.000	0.000	0.000
110	A	136	GLU	-2	-1.884	-1.910	11.994	-39.416	-39.416	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:27:LEU)